Liu Shiyong wrote:
Here is my command.
pdb2gmx -ignh -ff G53a6 -f b.pdb -p a6.top -i a6.posre.itp -o
a6.gro
pdb2gmx -ignh -ff G53a6 -f b.pdb -o a.pdb
Why are you running pdb2gmx twice? Unless you have multiple
proteins, and need multiple topologies, you should not be doing this.
That's because the *.gro file does not include chain id information.
If I run make_ndx -f a6.gro -o a6.ndx
I will get :
Found 0 atoms with chain identifiers A AND B
>
Found 0 atoms with chain identifier C
Alright, I was just confused why you're running pdb2gmx twice to get the desired
output. If you need a .pdb file, then just choose it as your output format the
first time you run the command. I would recommend not dealing with multiple
iterations of the same command; it can lead to confusion.
editconf -f a6.gro -o a6.gro -d 20.0
You realize that the units of -d are nm, right? Do you need such a
huge solute-box distance?
I know the units is nm.
Just checking :)
<snip>
-------------------------------------------------------
Program grompp, VERSION 4.0.2
Source code file: grompp.c, line: 150
Fatal error:
atoms 1 and 2 in charge group 1 of molecule type
'Protein_A' are
in different energy groups
-------------------------------------------------------
There is still some sort of disconnect between topology numbering (which is
where charge groups are defined), and the structure you are using. Can you post
the first *few* lines of your .pdb file, [ atoms ] section of the .top, and the
relevant index groups?
-Justin
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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